Everytime I try to query using an index, it stops using the indexes if I use two percentage signs. Why is that and what can I do?

do you mean

... WHERE foo LIKE '%bar%'

you can't do anything, it is in the nature of this construct that all values of foo must be examined, hence there's no point to using an index

the index will be used for this --

... WHERE foo LIKE 'bar%'

Well I'm trying to write a search engine for my site, what options do I have? Can I opimize the query or anything?

if you need to search all rows of the table to find those which match '%bar%' then that's already as optimized as you're gonna get